Difference between revisions of "Mutation effect on sites (analysis)"

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m (Protected "Mutation effect on sites (analysis)": Autogenerated page (‎[edit=sysop] (indefinite)))
(Automatic synchronization with BioUML)
 
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;Analysis title
 
;Analysis title
:[[File:BSA-Mutation-effect-on-sites-icon.png]] Mutation effect on sites
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:[[File:Mutations-Mutation-effect-on-sites-icon.png]] Mutation effect on sites
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|ru.biosoft.bsa.analysis.MutationEffectOnSites}}
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:{{Class|ru.biosoft.bsa.analysis.maos.MutationEffectOnSites}}
 
;Plugin
 
;Plugin
 
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
 
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
  
 
==== Description ====
 
==== Description ====
Find transcription factor binsing sites affected by mutations
+
Find transcription factor binding sites affected by mutations.
  
 
==== Parameters: ====
 
==== Parameters: ====
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** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
 
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
 
* '''Profile''' – Predefined set of site models
 
* '''Profile''' – Predefined set of site models
 +
* '''Score type''' – The type of position weight matrix score
 
* '''Score difference''' – Minimal site score difference between reference and alternative sequences
 
* '''Score difference''' – Minimal site score difference between reference and alternative sequences
* '''Output track''' – Track with affected sites
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* '''Independent variations''' – Treat each variation independently
 +
* '''Target gene TSS upstream''' – When searching for target genes, match TF binding sites to this distance upstream of TSS.
 +
* '''Target gene TSS downstream''' – When searching for target genes, match TF binding sites to this distance downstream of TSS.
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* '''One nearest target gene''' – Report only one target gene nearest to TSS.
 +
* '''Output table''' – Output table
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* '''Site gain track''' – Resulting track with site gain events
 +
* '''Site loss track''' – Resulting track with site gain events
 +
* '''Important mutations''' – Track of mutations that affects binding sites
 +
* '''Summary table''' – Summary table giving site model frequencies per mutation
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
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[[Category:Mutations (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
Mutations-Mutation-effect-on-sites-icon.png Mutation effect on sites
Provider
Institute of Systems Biology
Class
MutationEffectOnSites
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

[edit] Description

Find transcription factor binding sites affected by mutations.

[edit] Parameters:

  • Input VCF track – Input track in VCF format
  • Genome – Reference genome
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
  • Profile – Predefined set of site models
  • Score type – The type of position weight matrix score
  • Score difference – Minimal site score difference between reference and alternative sequences
  • Independent variations – Treat each variation independently
  • Target gene TSS upstream – When searching for target genes, match TF binding sites to this distance upstream of TSS.
  • Target gene TSS downstream – When searching for target genes, match TF binding sites to this distance downstream of TSS.
  • One nearest target gene – Report only one target gene nearest to TSS.
  • Output table – Output table
  • Site gain track – Resulting track with site gain events
  • Site loss track – Resulting track with site gain events
  • Important mutations – Track of mutations that affects binding sites
  • Summary table – Summary table giving site model frequencies per mutation
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